Summary plots - Sample strategy is on the y-axis and
number of sites is on the x-axis. Each plot is paired by parameter level
vertically and the values in the cells are the mean value across all of
the simulations for that parameter level. Note that each average
encompasses all of the other varying simulation parameters as seen in
the Full plots.
Full plots - For the full plots, Each plot
represents a unique simulation and the values in the cells are the mean
value across all of the 10 iterations of that simulation across all
three unique landscape seeds (i.e., all three sets of Neutral Landscape
Models) for a total of 30 replicates. Sample strategy is on the y-axis
and number of sites is on the x-axis. Since there are a many simulations
presented in the full plots, here is a handy key for how the different
parameters are laid out within them (H = High, L = Low):

TPR - True Positive Rate. The proportion of times
there was a positive detection in both the sub-sampled model and the
full model. Note that in the case of GDM TPR is frequently NA because
there was no detection in the full model.
FDR - False Discovery Rate. The proportion of times
there was a detection in the sub-sampled model that was not shared with
the full model.
ME - mean error was calculated by taking the mean
difference between the observed and expected coefficients, because the
absolute value is not taken this measurement is used to determine
whether over- or underestimation is occurring. For IBE ME the two
environmental coefficient errors were averaged.
MAE - mean absolute error calculated as the
difference between the observed and expected coefficients. For IBE MAE
the two environmental coefficient errors were averaged.
Proportion of negative & significant coefficients - this
only applies to MMRR and IBE and is the proportion of coefficients that
were negative & significant.
Proportion NA - this only applies to GDM and IBE and is the
proportion of NA p-values due to the variable significance procedure
note being able to be carried out because more than two variable
coefficients in the model were zero or because one of the models used in
the calculation could not be fit. Note that p-values would also be NA in
the case of the variable coefficient was zero, but we treated these as
cases of no detection in our calculation of TPR/FDR, whereas the other
NA values were excluded.
1. MMRR
1.1 Individual sampling
1.1.2 Linear mixed effects models
## Warning in run_lmer(mmrr_ind, .x, filepath = make_lmer_path("mmrr", "ind", :
## All values of IBD TPR are fixed or NA; no model is returned
## Warning in run_lmer(mmrr_ind, .x, filepath = make_lmer_path("mmrr", "ind", :
## All values of IBD FDR are fixed or NA; no model is returned
|
Linear mixed effect model
|
|
IBD MAE ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed)
|
|
Predictors
|
Fixed Effects
|
Sum Sq
|
Mean Sq
|
NumDF
|
DenDF
|
F value
|
Pr(>F)
|
|
Sample number
|
−0.0001
|
1.2256
|
1.2256
|
1
|
15.3480K
|
1239.45785
|
3.5 ×
10−261
|
|
Population size
|
0.0074
|
0.2110
|
0.2110
|
1
|
15.3480K
|
213.43225
|
5.1 ×
10−48
|
|
Migration
|
0.0255
|
2.5010
|
2.5010
|
1
|
15.3480K
|
2529.24460
|
0.0
|
|
Selection strength
|
−0.0017
|
0.0117
|
0.0117
|
1
|
15.3480K
|
11.86573
|
5.7 ×
10−4
|
|
Spatial autocorrelation
|
0.0060
|
0.1360
|
0.1360
|
1
|
15.3480K
|
137.55767
|
1.2 ×
10−31
|
|
Environmental correlation
|
−0.0017
|
0.0109
|
0.0109
|
1
|
15.3480K
|
11.04706
|
8.9 ×
10−4
|
|
Tukey test for IBD MAE
|
|
pairwise ~ sampstrat
|
|
Contrast
|
Estimate
|
SE
|
Z ratio
|
p
|
|
ES - G
|
−0.0029
|
0.0007
|
−4.0599
|
2.9 × 10−4
|
|
ES - R
|
−0.0010
|
0.0007
|
−1.4344
|
0.47776346
|
|
ES - T
|
−0.0246
|
0.0007
|
−34.3328
|
0.0
|
|
G - R
|
0.0019
|
0.0007
|
2.6255
|
0.04296249
|
|
G - T
|
−0.0217
|
0.0007
|
−30.2729
|
0.0
|
|
R - T
|
−0.0236
|
0.0007
|
−32.8984
|
0.0
|
|
Linear mixed effect model
|
|
IBE TPR ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed)
|
|
Predictors
|
Fixed Effects
|
Sum Sq
|
Mean Sq
|
NumDF
|
DenDF
|
F value
|
Pr(>F)
|
|
Sample number
|
0.0017
|
169.6446
|
169.6446
|
1
|
11.8600K
|
1368.252072
|
1.5 ×
10−283
|
|
Population size
|
−0.1035
|
31.5107
|
31.5107
|
1
|
11.8601K
|
254.146163
|
1.3 ×
10−56
|
|
Migration
|
−0.3584
|
330.2984
|
330.2984
|
1
|
11.8601K
|
2663.989576
|
0.0
|
|
Selection strength
|
0.0597
|
10.5688
|
10.5688
|
1
|
11.8601K
|
85.241941
|
3.1 ×
10−20
|
|
Spatial autocorrelation
|
0.3415
|
293.4664
|
293.4664
|
1
|
11.8603K
|
2366.924775
|
0.0
|
|
Environmental correlation
|
−0.0200
|
1.1842
|
1.1842
|
1
|
11.8600K
|
9.551297
|
2.0 ×
10−3
|
|
Tukey test for IBE TPR
|
|
pairwise ~ sampstrat
|
|
Contrast
|
Estimate
|
SE
|
Z ratio
|
p
|
|
ES - G
|
0.1269
|
0.0091
|
13.8781
|
0.0
|
|
ES - R
|
0.0756
|
0.0091
|
8.2753
|
4.5 × 10−14
|
|
ES - T
|
−0.0101
|
0.0091
|
−1.1058
|
0.6859408
|
|
G - R
|
−0.0512
|
0.0091
|
−5.6029
|
1.3 × 10−7
|
|
G - T
|
−0.1370
|
0.0091
|
−14.9840
|
0.0
|
|
R - T
|
−0.0857
|
0.0091
|
−9.3811
|
3.8 × 10−14
|
|
Linear mixed effect model
|
|
IBE FDR ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed)
|
|
Predictors
|
Fixed Effects
|
Sum Sq
|
Mean Sq
|
NumDF
|
DenDF
|
F value
|
Pr(>F)
|
|
Sample number
|
0.0001
|
1.0722
|
1.0722
|
1
|
15.3480K
|
46.924365
|
7.7 ×
10−12
|
|
Population size
|
0.0167
|
1.0667
|
1.0667
|
1
|
15.3480K
|
46.683954
|
8.7 ×
10−12
|
|
Migration
|
0.0182
|
1.2760
|
1.2760
|
1
|
15.3480K
|
55.847504
|
8.3 ×
10−14
|
|
Selection strength
|
−0.0036
|
0.0510
|
0.0510
|
1
|
15.3480K
|
2.233900
|
0.14
|
|
Spatial autocorrelation
|
−0.0413
|
6.5423
|
6.5423
|
1
|
15.3480K
|
286.329583
|
1.2 ×
10−63
|
|
Environmental correlation
|
0.0069
|
0.1829
|
0.1829
|
1
|
15.3480K
|
8.003859
|
4.7 ×
10−3
|
|
Tukey test for IBE FDR
|
|
pairwise ~ sampstrat
|
|
Contrast
|
Estimate
|
SE
|
Z ratio
|
p
|
|
ES - G
|
0.0103
|
0.0034
|
2.9819
|
0.01519496
|
|
ES - R
|
0.0052
|
0.0034
|
1.5098
|
0.43153409
|
|
ES - T
|
−0.0194
|
0.0034
|
−5.6240
|
1.1 × 10−7
|
|
G - R
|
−0.0051
|
0.0034
|
−1.4721
|
0.45448499
|
|
G - T
|
−0.0297
|
0.0034
|
−8.6058
|
3.6 × 10−14
|
|
R - T
|
−0.0246
|
0.0034
|
−7.1338
|
5.9 × 10−12
|
|
Linear mixed effect model
|
|
IBE MAE ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed)
|
|
Predictors
|
Fixed Effects
|
Sum Sq
|
Mean Sq
|
NumDF
|
DenDF
|
F value
|
Pr(>F)
|
|
Sample number
|
−0.0002
|
2.4101
|
2.4101
|
1
|
15.3480K
|
3606.434014
|
0.0
|
|
Population size
|
0.0037
|
0.0526
|
0.0526
|
1
|
15.3480K
|
78.639576
|
8.3 ×
10−19
|
|
Migration
|
0.0178
|
1.2102
|
1.2102
|
1
|
15.3480K
|
1810.842798
|
0.0
|
|
Selection strength
|
−0.0019
|
0.0134
|
0.0134
|
1
|
15.3480K
|
20.109804
|
7.4 ×
10−6
|
|
Spatial autocorrelation
|
0.0025
|
0.0241
|
0.0241
|
1
|
15.3480K
|
36.110285
|
1.9 ×
10−9
|
|
Environmental correlation
|
0.0007
|
0.0020
|
0.0020
|
1
|
15.3480K
|
2.978678
|
0.084
|
|
Tukey test for IBE MAE
|
|
pairwise ~ sampstrat
|
|
Contrast
|
Estimate
|
SE
|
Z ratio
|
p
|
|
ES - G
|
0.0014
|
0.0006
|
2.3636
|
0.08420456
|
|
ES - R
|
0.0022
|
0.0006
|
3.6842
|
1.3 × 10−3
|
|
ES - T
|
−0.0041
|
0.0006
|
−6.9400
|
2.4 × 10−11
|
|
G - R
|
0.0008
|
0.0006
|
1.3206
|
0.54973652
|
|
G - T
|
−0.0055
|
0.0006
|
−9.3037
|
4.1 × 10−14
|
|
R - T
|
−0.0063
|
0.0006
|
−10.6243
|
3.6 × 10−14
|
1.2 Site sampling
1.2.2 Linear mixed effects models
|
Linear mixed effect model
|
|
IBD TPR ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed)
|
|
Predictors
|
Fixed Effects
|
Sum Sq
|
Mean Sq
|
NumDF
|
DenDF
|
F value
|
Pr(>F)
|
|
Sample number
|
0.0001
|
0.0080
|
0.0080
|
1
|
8.6310K
|
8.619034e+00
|
3.3 ×
10−3
|
|
Population size
|
−0.0009
|
0.0019
|
0.0019
|
1
|
8.6310K
|
2.003506e+00
|
0.16
|
|
Migration
|
−0.0009
|
0.0019
|
0.0019
|
1
|
8.6310K
|
2.003506e+00
|
0.16
|
|
Selection strength
|
0.0005
|
0.0005
|
0.0005
|
1
|
8.6310K
|
5.008765e-01
|
0.48
|
|
Spatial autocorrelation
|
−0.0009
|
0.0019
|
0.0019
|
1
|
8.6310K
|
2.003506e+00
|
0.16
|
|
Environmental correlation
|
0.0000
|
0.0000
|
0.0000
|
1
|
8.6310K
|
4.154190e-25
|
1.00
|
|
Tukey test for IBD TPR
|
|
pairwise ~ sampstrat
|
|
Contrast
|
Estimate
|
SE
|
Z ratio
|
p
|
|
EQ - ES
|
0.0007
|
0.0008
|
0.8668
|
0.6612852
|
|
EQ - R
|
0.0000
|
0.0008
|
0.0000
|
1.0000000
|
|
ES - R
|
−0.0007
|
0.0008
|
−0.8668
|
0.6612852
|
## Warning in run_lmer(mmrr_site, .x, filepath = make_lmer_path("mmrr", "site", :
## All values of IBD FDR are fixed or NA; no model is returned
|
Linear mixed effect model
|
|
IBD MAE ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed)
|
|
Predictors
|
Fixed Effects
|
Sum Sq
|
Mean Sq
|
NumDF
|
DenDF
|
F value
|
Pr(>F)
|
|
Sample number
|
−0.0010
|
0.3624
|
0.3624
|
1
|
8.6290K
|
1.989363e+02
|
1.1 ×
10−44
|
|
Population size
|
0.0221
|
1.0570
|
1.0570
|
1
|
8.6290K
|
5.802786e+02
|
3.8 ×
10−124
|
|
Migration
|
0.1068
|
24.6577
|
24.6577
|
1
|
8.6290K
|
1.353681e+04
|
0.0
|
|
Selection strength
|
−0.0075
|
0.1219
|
0.1219
|
1
|
8.6290K
|
6.693473e+01
|
3.2 ×
10−16
|
|
Spatial autocorrelation
|
−0.0002
|
0.0001
|
0.0001
|
1
|
8.6290K
|
6.310007e-02
|
0.80
|
|
Environmental correlation
|
0.0012
|
0.0033
|
0.0033
|
1
|
8.6290K
|
1.784720e+00
|
0.18
|
|
Tukey test for IBD MAE
|
|
pairwise ~ sampstrat
|
|
Contrast
|
Estimate
|
SE
|
Z ratio
|
p
|
|
EQ - ES
|
0.0000
|
0.0011
|
−0.0428
|
0.9989921
|
|
EQ - R
|
−0.0038
|
0.0011
|
−3.3592
|
2.3 × 10−3
|
|
ES - R
|
−0.0037
|
0.0011
|
−3.3164
|
2.6 × 10−3
|
|
Linear mixed effect model
|
|
IBE TPR ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed)
|
|
Predictors
|
Fixed Effects
|
Sum Sq
|
Mean Sq
|
NumDF
|
DenDF
|
F value
|
Pr(>F)
|
|
Sample number
|
0.0090
|
23.0011
|
23.0011
|
1
|
6.6670K
|
259.6127162
|
2.5 ×
10−57
|
|
Population size
|
0.0028
|
0.0127
|
0.0127
|
1
|
6.6674K
|
0.1430862
|
0.710
|
|
Migration
|
−0.0046
|
0.0309
|
0.0309
|
1
|
6.6673K
|
0.3491155
|
0.550
|
|
Selection strength
|
0.0157
|
0.4098
|
0.4098
|
1
|
6.6673K
|
4.6251140
|
0.032
|
|
Spatial autocorrelation
|
0.0818
|
9.4689
|
9.4689
|
1
|
6.6681K
|
106.8752726
|
7.3 ×
10−25
|
|
Environmental correlation
|
−0.0321
|
1.7169
|
1.7169
|
1
|
6.6671K
|
19.3781699
|
1.1 ×
10−5
|
|
Tukey test for IBE TPR
|
|
pairwise ~ sampstrat
|
|
Contrast
|
Estimate
|
SE
|
Z ratio
|
p
|
|
EQ - ES
|
−0.1357
|
0.0089
|
−15.2061
|
0.0
|
|
EQ - R
|
−0.0883
|
0.0089
|
−9.8940
|
2.8 × 10−14
|
|
ES - R
|
0.0474
|
0.0089
|
5.3121
|
3.2 × 10−7
|
|
Linear mixed effect model
|
|
IBE FDR ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed)
|
|
Predictors
|
Fixed Effects
|
Sum Sq
|
Mean Sq
|
NumDF
|
DenDF
|
F value
|
Pr(>F)
|
|
Sample number
|
0.0007
|
0.1970
|
0.1970
|
1
|
8.6290K
|
12.054216
|
5.2 ×
10−4
|
|
Population size
|
0.0105
|
0.2396
|
0.2396
|
1
|
8.6290K
|
14.663682
|
1.3 ×
10−4
|
|
Migration
|
0.0378
|
3.0940
|
3.0940
|
1
|
8.6290K
|
189.345838
|
1.2 ×
10−42
|
|
Selection strength
|
−0.0047
|
0.0486
|
0.0486
|
1
|
8.6290K
|
2.976651
|
0.085
|
|
Spatial autocorrelation
|
−0.0337
|
2.4503
|
2.4503
|
1
|
8.6290K
|
149.949919
|
3.4 ×
10−34
|
|
Environmental correlation
|
0.0073
|
0.1148
|
0.1148
|
1
|
8.6290K
|
7.028155
|
8.0 ×
10−3
|
|
Tukey test for IBE FDR
|
|
pairwise ~ sampstrat
|
|
Contrast
|
Estimate
|
SE
|
Z ratio
|
p
|
|
EQ - ES
|
−0.0175
|
0.0034
|
−5.2053
|
5.8 × 10−7
|
|
EQ - R
|
−0.0066
|
0.0034
|
−1.9584
|
0.1226645
|
|
ES - R
|
0.0109
|
0.0034
|
3.2469
|
3.3 × 10−3
|
|
Linear mixed effect model
|
|
IBE MAE ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed)
|
|
Predictors
|
Fixed Effects
|
Sum Sq
|
Mean Sq
|
NumDF
|
DenDF
|
F value
|
Pr(>F)
|
|
Sample number
|
−0.0027
|
2.7352
|
2.7352
|
1
|
8.6290K
|
1.622508e+03
|
0.0
|
|
Population size
|
0.0014
|
0.0045
|
0.0045
|
1
|
8.6290K
|
2.682024e+00
|
0.10
|
|
Migration
|
0.0071
|
0.1102
|
0.1102
|
1
|
8.6290K
|
6.539688e+01
|
7.0 ×
10−16
|
|
Selection strength
|
−0.0001
|
0.0000
|
0.0000
|
1
|
8.6290K
|
8.222296e-03
|
0.93
|
|
Spatial autocorrelation
|
0.0036
|
0.0284
|
0.0284
|
1
|
8.6290K
|
1.686173e+01
|
4.1 ×
10−5
|
|
Environmental correlation
|
0.0062
|
0.0833
|
0.0833
|
1
|
8.6290K
|
4.941667e+01
|
2.2 ×
10−12
|
|
Tukey test for IBE MAE
|
|
pairwise ~ sampstrat
|
|
Contrast
|
Estimate
|
SE
|
Z ratio
|
p
|
|
EQ - ES
|
0.0004
|
0.0011
|
0.3705
|
0.9271412
|
|
EQ - R
|
0.0049
|
0.0011
|
4.5248
|
1.8 × 10−5
|
|
ES - R
|
0.0045
|
0.0011
|
4.1543
|
9.7 × 10−5
|
2. GDM
2.1 Individual sampling
2.1.2 Linear mixed effects models
## Warning in run_lmer(gdm_ind, .x, filepath = make_lmer_path("gdm", "ind", :
## All values of IBD TPR are fixed or NA; no model is returned
## Warning in run_lmer(gdm_ind, .x, filepath = make_lmer_path("gdm", "ind", :
## All values of IBD FDR are fixed or NA; no model is returned
|
Linear mixed effect model
|
|
IBD MAE ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed)
|
|
Predictors
|
Fixed Effects
|
Sum Sq
|
Mean Sq
|
NumDF
|
DenDF
|
F value
|
Pr(>F)
|
|
Sample number
|
−0.0003
|
4.9829
|
4.9829
|
1
|
15.3420K
|
2555.862541
|
0.0
|
|
Population size
|
0.0019
|
0.0142
|
0.0142
|
1
|
15.3420K
|
7.279726
|
7.0 ×
10−3
|
|
Migration
|
−0.0145
|
0.8120
|
0.8120
|
1
|
15.3420K
|
416.506452
|
2.3 ×
10−91
|
|
Selection strength
|
−0.0008
|
0.0026
|
0.0026
|
1
|
15.3420K
|
1.311347
|
0.250
|
|
Spatial autocorrelation
|
0.0008
|
0.0025
|
0.0025
|
1
|
15.3420K
|
1.293043
|
0.260
|
|
Environmental correlation
|
0.0014
|
0.0074
|
0.0074
|
1
|
15.3420K
|
3.816871
|
0.051
|
|
Tukey test for IBD MAE
|
|
pairwise ~ sampstrat
|
|
Contrast
|
Estimate
|
SE
|
Z ratio
|
p
|
|
ES - G
|
0.0168
|
0.0010
|
16.6615
|
0.0
|
|
ES - R
|
0.0049
|
0.0010
|
4.8334
|
8.0 × 10−6
|
|
ES - T
|
0.0094
|
0.0010
|
9.3011
|
4.1 × 10−14
|
|
G - R
|
−0.0119
|
0.0010
|
−11.8249
|
0.0
|
|
G - T
|
−0.0074
|
0.0010
|
−7.3615
|
1.1 × 10−12
|
|
R - T
|
0.0045
|
0.0010
|
4.4656
|
4.7 × 10−5
|
## Warning in run_lmer(gdm_ind, .x, filepath = make_lmer_path("gdm", "ind", :
## All values of env_p_TPR are NA for a level of H ; this parameter is dropped from the model
|
Linear mixed effect model
|
|
IBE TPR ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed)
|
|
Predictors
|
Fixed Effects
|
Sum Sq
|
Mean Sq
|
NumDF
|
DenDF
|
F value
|
Pr(>F)
|
|
Sample number
|
0.0009
|
2.3033
|
2.3033
|
1
|
498.2415
|
42.0843063
|
2.1 ×
10−10
|
|
Population size
|
−0.1315
|
0.8938
|
0.8938
|
1
|
451.8375
|
16.3300295
|
6.3 ×
10−5
|
|
Migration
|
−0.1162
|
1.0973
|
1.0973
|
1
|
492.1461
|
20.0498258
|
9.4 ×
10−6
|
|
Selection strength
|
0.0316
|
0.1192
|
0.1192
|
1
|
499.4142
|
2.1784099
|
0.14
|
|
Environmental correlation
|
−0.0218
|
0.0508
|
0.0508
|
1
|
499.1400
|
0.9284533
|
0.34
|
|
Tukey test for IBE TPR
|
|
pairwise ~ sampstrat
|
|
Contrast
|
Estimate
|
SE
|
t ratio
|
p
|
|
ES - G
|
0.0633
|
0.0293
|
2.1597
|
0.13606967
|
|
ES - R
|
−0.0152
|
0.0294
|
−0.5179
|
0.95477772
|
|
ES - T
|
−0.0773
|
0.0293
|
−2.6394
|
0.04243910
|
|
G - R
|
−0.0785
|
0.0294
|
−2.6743
|
0.03860818
|
|
G - T
|
−0.1406
|
0.0292
|
−4.8088
|
1.2 × 10−5
|
|
R - T
|
−0.0621
|
0.0294
|
−2.1150
|
0.14971246
|
|
Linear mixed effect model
|
|
IBE FDR ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed)
|
|
Predictors
|
Fixed Effects
|
Sum Sq
|
Mean Sq
|
NumDF
|
DenDF
|
F value
|
Pr(>F)
|
|
Sample number
|
0.0001
|
0.6559
|
0.6559
|
1
|
14.6290K
|
67.005997
|
2.9 ×
10−16
|
|
Population size
|
−0.0057
|
0.1201
|
0.1201
|
1
|
14.6291K
|
12.268760
|
4.6 ×
10−4
|
|
Migration
|
−0.0032
|
0.0379
|
0.0379
|
1
|
14.6291K
|
3.875703
|
0.049
|
|
Selection strength
|
0.0020
|
0.0149
|
0.0149
|
1
|
14.6294K
|
1.521359
|
0.220
|
|
Spatial autocorrelation
|
0.0095
|
0.3276
|
0.3276
|
1
|
14.6292K
|
33.469328
|
7.4 ×
10−9
|
|
Environmental correlation
|
−0.0026
|
0.0240
|
0.0240
|
1
|
14.6291K
|
2.454630
|
0.120
|
|
Tukey test for IBE FDR
|
|
pairwise ~ sampstrat
|
|
Contrast
|
Estimate
|
SE
|
Z ratio
|
p
|
|
ES - G
|
0.0044
|
0.0023
|
1.9074
|
0.2248336
|
|
ES - R
|
−0.0037
|
0.0023
|
−1.5989
|
0.3791959
|
|
ES - T
|
−0.0161
|
0.0023
|
−6.9828
|
1.7 × 10−11
|
|
G - R
|
−0.0081
|
0.0023
|
−3.5077
|
2.5 × 10−3
|
|
G - T
|
−0.0205
|
0.0023
|
−8.9047
|
2.8 × 10−14
|
|
R - T
|
−0.0124
|
0.0023
|
−5.3768
|
4.5 × 10−7
|
|
Linear mixed effect model
|
|
IBE MAE ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed)
|
|
Predictors
|
Fixed Effects
|
Sum Sq
|
Mean Sq
|
NumDF
|
DenDF
|
F value
|
Pr(>F)
|
|
Sample number
|
−0.0001
|
0.3139
|
0.3139
|
1
|
15.3420K
|
1854.72544
|
0.0
|
|
Population size
|
−0.0024
|
0.0220
|
0.0220
|
1
|
15.3420K
|
129.70282
|
6.3 ×
10−30
|
|
Migration
|
0.0014
|
0.0070
|
0.0070
|
1
|
15.3420K
|
41.59368
|
1.2 ×
10−10
|
|
Selection strength
|
0.0015
|
0.0084
|
0.0084
|
1
|
15.3420K
|
49.43952
|
2.1 ×
10−12
|
|
Spatial autocorrelation
|
0.0014
|
0.0076
|
0.0076
|
1
|
15.3420K
|
44.82430
|
2.2 ×
10−11
|
|
Environmental correlation
|
−0.0011
|
0.0044
|
0.0044
|
1
|
15.3420K
|
26.19737
|
3.1 ×
10−7
|
|
Tukey test for IBE MAE
|
|
pairwise ~ sampstrat
|
|
Contrast
|
Estimate
|
SE
|
Z ratio
|
p
|
|
ES - G
|
−0.0009
|
0.0003
|
−3.0951
|
0.01060546
|
|
ES - R
|
−0.0019
|
0.0003
|
−6.3196
|
1.6 × 10−9
|
|
ES - T
|
−0.0027
|
0.0003
|
−8.9634
|
2.7 × 10−14
|
|
G - R
|
−0.0010
|
0.0003
|
−3.2251
|
6.9 × 10−3
|
|
G - T
|
−0.0017
|
0.0003
|
−5.8680
|
2.6 × 10−8
|
|
R - T
|
−0.0008
|
0.0003
|
−2.6416
|
0.04111901
|
2.1.4 Failed fits
Occasionally GDM fails to fit a model, in which case an NA value
is assigned. Here we check the proportion of NAs (i.e., cases of failed
fit) across the simulations:
Proportion of failed full models:

2.2 Site sampling
2.2.2 Linear mixed effects models
|
Linear mixed effect model
|
|
IBD TPR ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed)
|
|
Predictors
|
Fixed Effects
|
Sum Sq
|
Mean Sq
|
NumDF
|
DenDF
|
F value
|
Pr(>F)
|
|
Sample number
|
0.0005
|
0.0811
|
0.0811
|
1
|
7.8090K
|
30.38402362
|
3.7 ×
10−8
|
|
Population size
|
0.0007
|
0.0010
|
0.0010
|
1
|
7.8090K
|
0.38176437
|
0.54
|
|
Migration
|
−0.0003
|
0.0001
|
0.0001
|
1
|
7.8090K
|
0.05418347
|
0.82
|
|
Selection strength
|
−0.0016
|
0.0052
|
0.0052
|
1
|
7.8090K
|
1.94232427
|
0.16
|
|
Spatial autocorrelation
|
−0.0015
|
0.0044
|
0.0044
|
1
|
7.8090K
|
1.64653123
|
0.20
|
|
Environmental correlation
|
−0.0008
|
0.0013
|
0.0013
|
1
|
7.8090K
|
0.50243692
|
0.48
|
|
Tukey test for IBD TPR
|
|
pairwise ~ sampstrat
|
|
Contrast
|
Estimate
|
SE
|
Z ratio
|
p
|
|
EQ - ES
|
−0.0017
|
0.0014
|
−1.2089
|
0.4478540
|
|
EQ - R
|
−0.0025
|
0.0014
|
−1.7343
|
0.1924110
|
|
ES - R
|
−0.0008
|
0.0014
|
−0.5245
|
0.8593617
|
## Warning in run_lmer(gdm_site, .x, filepath = make_lmer_path("gdm", "site", :
## All values of IBD FDR are fixed or NA; no model is returned
|
Linear mixed effect model
|
|
IBD MAE ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed)
|
|
Predictors
|
Fixed Effects
|
Sum Sq
|
Mean Sq
|
NumDF
|
DenDF
|
F value
|
Pr(>F)
|
|
Sample number
|
−0.0017
|
1.0608
|
1.0608
|
1
|
8.4000K
|
171.818434
|
7.1 ×
10−39
|
|
Population size
|
0.0154
|
0.4994
|
0.4994
|
1
|
8.4000K
|
80.890799
|
2.9 ×
10−19
|
|
Migration
|
0.0868
|
15.8373
|
15.8373
|
1
|
8.4000K
|
2565.095054
|
0.0
|
|
Selection strength
|
−0.0036
|
0.0271
|
0.0271
|
1
|
8.4000K
|
4.382271
|
0.036
|
|
Spatial autocorrelation
|
−0.0030
|
0.0191
|
0.0191
|
1
|
8.4000K
|
3.096860
|
0.078
|
|
Environmental correlation
|
0.0057
|
0.0679
|
0.0679
|
1
|
8.4001K
|
11.001157
|
9.1 ×
10−4
|
|
Tukey test for IBD MAE
|
|
pairwise ~ sampstrat
|
|
Contrast
|
Estimate
|
SE
|
Z ratio
|
p
|
|
EQ - ES
|
−0.0295
|
0.0021
|
−14.0721
|
0.0
|
|
EQ - R
|
−0.0288
|
0.0021
|
−13.7786
|
0.0
|
|
ES - R
|
0.0006
|
0.0021
|
0.2962
|
0.9527765
|
## Warning in run_lmer(gdm_site, .x, filepath = make_lmer_path("gdm", "site", :
## All values of env_p_TPR are NA for a level of H ; this parameter is dropped from the model
|
Linear mixed effect model
|
|
IBE TPR ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed)
|
|
Predictors
|
Fixed Effects
|
Sum Sq
|
Mean Sq
|
NumDF
|
DenDF
|
F value
|
Pr(>F)
|
|
Sample number
|
0.0017
|
0.0308
|
0.0308
|
1
|
255.6048
|
2.1991749
|
0.14
|
|
Population size
|
−0.0320
|
0.0281
|
0.0281
|
1
|
231.6609
|
2.0046388
|
0.16
|
|
Migration
|
−0.0105
|
0.0046
|
0.0046
|
1
|
255.3889
|
0.3271284
|
0.57
|
|
Selection strength
|
−0.0096
|
0.0056
|
0.0056
|
1
|
256.8676
|
0.4026111
|
0.53
|
|
Environmental correlation
|
−0.0115
|
0.0074
|
0.0074
|
1
|
255.6449
|
0.5268093
|
0.47
|
|
Tukey test for IBE TPR
|
|
pairwise ~ sampstrat
|
|
Contrast
|
Estimate
|
SE
|
t ratio
|
p
|
|
EQ - ES
|
−0.0464
|
0.0177
|
−2.6220
|
0.02503871
|
|
EQ - R
|
−0.0345
|
0.0178
|
−1.9449
|
0.12832970
|
|
ES - R
|
0.0119
|
0.0181
|
0.6564
|
0.78892520
|
|
Linear mixed effect model
|
|
IBE FDR ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed)
|
|
Predictors
|
Fixed Effects
|
Sum Sq
|
Mean Sq
|
NumDF
|
DenDF
|
F value
|
Pr(>F)
|
|
Sample number
|
0.0004
|
0.0424
|
0.0424
|
1
|
7.6355K
|
9.259080
|
2.4 ×
10−3
|
|
Population size
|
0.0026
|
0.0132
|
0.0132
|
1
|
7.6350K
|
2.890448
|
0.089
|
|
Migration
|
0.0022
|
0.0092
|
0.0092
|
1
|
7.6350K
|
2.016252
|
0.160
|
|
Selection strength
|
0.0031
|
0.0184
|
0.0184
|
1
|
7.6351K
|
4.019454
|
0.045
|
|
Spatial autocorrelation
|
0.0087
|
0.1444
|
0.1444
|
1
|
7.6352K
|
31.538566
|
2.0 ×
10−8
|
|
Environmental correlation
|
−0.0037
|
0.0257
|
0.0257
|
1
|
7.6352K
|
5.620700
|
0.018
|
|
Tukey test for IBE FDR
|
|
pairwise ~ sampstrat
|
|
Contrast
|
Estimate
|
SE
|
Z ratio
|
p
|
|
EQ - ES
|
−0.0086
|
0.0019
|
−4.5867
|
1.3 × 10−5
|
|
EQ - R
|
−0.0067
|
0.0019
|
−3.5419
|
1.2 × 10−3
|
|
ES - R
|
0.0019
|
0.0019
|
0.9936
|
0.5809158
|
|
Linear mixed effect model
|
|
IBE MAE ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed)
|
|
Predictors
|
Fixed Effects
|
Sum Sq
|
Mean Sq
|
NumDF
|
DenDF
|
F value
|
Pr(>F)
|
|
Sample number
|
−0.0008
|
0.2456
|
0.2456
|
1
|
8.4000K
|
637.0438734
|
1.5 ×
10−135
|
|
Population size
|
−0.0004
|
0.0003
|
0.0003
|
1
|
8.4000K
|
0.6935302
|
0.40
|
|
Migration
|
0.0021
|
0.0093
|
0.0093
|
1
|
8.4000K
|
24.2065506
|
8.8 ×
10−7
|
|
Selection strength
|
0.0002
|
0.0001
|
0.0001
|
1
|
8.4000K
|
0.2126786
|
0.64
|
|
Spatial autocorrelation
|
0.0040
|
0.0339
|
0.0339
|
1
|
8.4000K
|
87.9145144
|
8.6 ×
10−21
|
|
Environmental correlation
|
−0.0021
|
0.0090
|
0.0090
|
1
|
8.4000K
|
23.2593102
|
1.4 ×
10−6
|
|
Tukey test for IBE MAE
|
|
pairwise ~ sampstrat
|
|
Contrast
|
Estimate
|
SE
|
Z ratio
|
p
|
|
EQ - ES
|
0.0006
|
0.0005
|
1.1181
|
0.5028702
|
|
EQ - R
|
−0.0003
|
0.0005
|
−0.5903
|
0.8253362
|
|
ES - R
|
−0.0009
|
0.0005
|
−1.6922
|
0.2081436
|
2.2.4 Failed fits
Occasionally GDM fails to fit a model, in which case an NA value
is assigned. Here we check the proportion of NAs (i.e., cases of failed
fit) across the simulations:
Proportion of failed models:

Comparison of MMRR and GDM



Comparison of average IBE error:
## [1] "MMRR average IBE error: 0.04"
## [1] "GDM average IBE error: 0.02"